Cascade-mediated binding and bending of negatively supercoiled DNA

RNA Biology

Volumn 9, Issue 9, 2012, Pages 1134-1138

  Westra, Edze R ^a   Nilges, Benedikt ^a   Van Erp, Paul B G ^a   Van Der Oost, John ^a   Dame, Remus T ^b   Brouns, Stan J J ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b LEIDEN UNIVERSITY   (Netherlands)

Author keywords

Bacteria; CRISPR; Defense; DNA; Immune; Nucleic acids; Phage; Prokaryotes; Ribonucleoprotein complex; RNA

Indexed keywords

EID: 84868125172     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.21410     Document Type: Note

References (31)

1. Brouns SJJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJH, Snijders APL, et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 2008; 321:960-4; PMID:18703739; http://dx.doi.org/10.1126/science.1159689.
2. Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, et al. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol 2011; 18:529-36; PMID:21460843; http://dx.doi.org/10.1038/nsmb. 2019.
3. Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, et al. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc Natl Acad Sci USA 2011; 108:10098-103; PMID:21646539; http://dx.doi.org/10.1073/pnas.1104144108.
4. Westra ER, van Erp PB, Künne T, Wong SP, Staals RH, Seegers CL, et al. CRISPR Immunity Relies on the Consecutive Binding and Degradation of Negatively Supercoiled Invader DNA by Cascade and Cas3. Mol Cell 2012; 46:595-605; PMID:22521689; http://dx.doi.org/10.1016/j.molcel.2012.03.018.
5. Sashital DG, Wiedenheft B, Doudna JA. Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol Cell 2012; 46:606-15; PMID:22521690; http://dx.doi.org/10.1016/j.mol-cel.2012.03.020.
6. Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJ, van der Oost J, et al. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 2011; 477:486-9; PMID:21938068; http://dx.doi.org/10.1038/ nature10402.
7. Bhaya D, Davison M, Barrangou R. CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet 2011; 45:273-97; PMID:22060043; http://dx.doi.org/10.1146/annurev-genet- 110410-132430.
8. Wiedenheft B, Sternberg SH, Doudna JA. RNA-guided genetic silencing systems in bacteria and archaea. Nature 2012; 482:331-8; PMID:22337052; http://dx.doi.org/10.1038/nature10886.
9. Al-Attar S, Westra ER, van der Oost J, Brouns SJ. Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes. Biol Chem 2011; 392:277-89; PMID:21294681; http://dx.doi.org/10.1515/bc.2011.042.
10. Deveau H, Garneau JE, Moineau S. CRISPR/Cas system and its role in phage-bacteria interactions. Annu Rev Microbiol 2010; 64:475-93; PMID:20528693; http://dx.doi.org/10.1146/annurev.micro.112408.134123.
11. Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science 2010; 327:167-70; PMID:20056882; http://dx.doi.org/10.1126/ science.1179555.
12. Jore MM, Brouns SJ, van der Oost J. RNA in defense: CRISPRs protect prokaryotes against mobile genetic elements. Cold Spring Harb Perspect Biol 2012; 4:1-12; PMID:21441598; http://dx.doi.org/10.1101/cshperspect.a003657.
13. Karginov FV, Hannon GJ. The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol Cell 2010; 37:7-19; PMID:20129051; http://dx.doi.org/10.1016/j.molcel.2009.12.033.
14. Labrie SJ, Samson JE, Moineau S. Bacteriophage resistance mechanisms. Nat Rev Microbiol 2010; 8:317-27; PMID:20348932; http://dx.doi.org/10.1038/ nrmicro2315.
15. Marraffini LA, Sontheimer EJ. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 2010; 11:181-90; PMID:20125085; http://dx.doi.org/10.1038/nrg2749.
16. Terns MP, Terns RM. CRISPR-based adaptive immune systems. Curr Opin Microbiol 2011; 14:321-7; PMID:21531607; http://dx.doi.org/10.1016/j.mib.2011. 03.005.
17. van der Oost J, Jore MM, Westra ER, Lundgren M, Brouns SJJ. CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci 2009; 34:401-7; PMID:19646880; http://dx.doi.org/10.1016/j.tibs.2009.05.002.
18. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, et al. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 2011; 9:467-77; PMID:21552286; http://dx.doi.org/10.1038/nrmicro2577.
19. Kunin V, Sorek R, Hugenholtz P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol 2007; 8:R61; PMID:17442114; http://dx.doi.org/10.1186/gb-2007-8-4-r61.
20. Swarts DC, Mosterd C, van Passel MW, Brouns SJ. CRISPR interference directs strand specific spacer acquisition. PLoS One 2012; 7:e35888; PMID:22558257; http://dx.doi.org/10.1371/journal.pone.0035888.
21. Yosef I, Goren MG, Qimron U. Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res 2012; 40:5569-76; PMID:22402487; http://dx.doi.org/10.1093/nar/gks216.
22. Mojica FJM, Díez-Villaseñor C, García-Martínez J, Almendros C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 2009; 155:733-40; PMID:19246744; http://dx.doi.org/10.1099/mic.0.023960-0.
23. Sashital DG, Jinek M, Doudna JA. An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nat Struct Mol Biol 2011; 18:680-7; PMID:21572442; http://dx.doi.org/10.1038/nsmb.2043.
24. Gesner EM, Schellenberg MJ, Garside EL, George MM, Macmillan AM. Recognition and maturation of effector RNAs in a CRISPR interference pathway. Nat Struct Mol Biol 2011; 18:688-92; PMID:21572444; http://dx.doi.org/10.1038/ nsmb.2042.
25. Westra ER, Pul U, Heidrich N, Jore MM, Lundgren M, Stratmann T, et al. H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO. Mol Microbiol 2010; 77:1380-93; PMID:20659289; http://dx.doi.org/10.1111/j.1365-2958.2010.07315.x.
26. Agari Y, Yokoyama S, Kuramitsu S, Shinkai A. X-ray crystal structure of a CRISPR-associated protein, Cse2, from Thermus thermophilus HB8. Proteins 2008; 73:1063-7; PMID:18798563; http://dx.doi.org/10.1002/prot.22224.
27. Verhoeven EE, Wyman C, Moolenaar GF, Hoeijmakers JH, Goosen N. Architecture of nucleo-tide excision repair complexes: DNA is wrapped by UvrB before and after damage recognition. EMBO J 2001; 20:601-11; PMID:11157766; http://dx.doi.org/10.1093/emboj/20.3.601. (Pubitemid 32126995)
28. Dame RT, Wyman C, Wurm R, Wagner R, Goosen N. Structural basis for H-NS-mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1. J Biol Chem 2002; 277:2146-50; PMID:11714691; http://dx.doi.org/10. 1074/jbc.C100603200. (Pubitemid 34968800)
29. Dame RT, van Mameren J, Luijsterburg MS, Mysiak ME, Janicijevic A, Pazdzior G, et al. Analysis of scanning force microscopy images of protein-induced DNA bending using simulations. Nucleic Acids Res 2005; 33:e68; PMID:15843682; http://dx.doi.org/10.1093/nar/gni073.
30. van Noort J, Verbrugge S, Goosen N, Dekker C, Dame RT. Dual architectural roles of HU: formation of flexible hinges and rigid filaments. Proc Natl Acad Sci USA 2004; 101:6969-74; PMID:15118104; http://dx.doi.org/10.1073/pnas. 0308230101. (Pubitemid 38596427)
31. Zhang J, McCauley MJ, Maher LJ, Williams MC, Israeloff NE. Mechanism of DNA flexibility enhancement by HMGB proteins. Nucleic Acids Res 2009; 37:1107-14; PMID:19129233; http://dx.doi.org/10.1093/nar/gkn1011.